trans-2,5-Di­methyl­piperazine-1,4-diium bis(perchlorate) dihydrate: crystal structure and Hirshfeld surface analysis

The extended structure consists of infinite [010] chains linked by O_w—H⋯O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N—H⋯O_w and weak C—H⋯O hydrogen bonds, thus forming a three-dimensional supra­molecular network. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint maps reveal that the structure is dominated by H⋯O/O⋯H and H⋯H contacts.

Abstract

The asymmetric unit of the title hydrated mol­ecular salt, C₆H₁₆N₂ ²⁺·2ClO₄ ⁻·2H₂O, contains a half dication (completed by inversion symmetry), a perchlorate anion and a water mol­ecule. The extended structure consists of infinite chains of formula [(ClO₄)H₂O]_n^{n −} ions extending along the b axis linked by O_w—H⋯O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N—H⋯O_w and weak C—H⋯O hydrogen bonds, thus forming a three-dimensional supra­molecular network. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint maps reveal that the structure is dominated by H⋯O/O⋯H and H⋯H contacts.

Chemical context  

Piperazine (C₄H₁₀N₂) and its derivatives are a family of strongly basic amines able to form dications, in which all of the N—H bonds are generally active in hydrogen-bond formation. They are used in pharmacology and found in biologically active compounds across a number of different therapeutic areas, displaying anti­bacterial, anti­fungal, anti­malarial, anti­psychotic, anti­depressant and anti­tumor activity (Brockunier et al., 2004 ▸; Bogatcheva et al., 2006 ▸).

In this work, as part of our studies in this area, we report the preparation and structural investigation of a new hydrated perchlorate salt, C₆H₁₆N₂ ²⁺·2ClO₄ ⁻·2H₂O (I).

Structural commentary  

The asymmetric unit of (I) is composed of a half of a trans-2,5-dimethylpipeazine-1,4-dium dication, one perchlorate anion and one water mol­ecule (Fig. 1 ▸). The complete dication is generated by crystallographic inversion symmetry, leading to a typical chair conformation, with the methyl groups occupying equatorial positions [puckering parameters: Q = 0.7341 Å, θ = 90 and φ = −16 °], which is similar the conformation of the same species in its nitrate salt (Gatfaoui et al., 2014 ▸). Otherwise, the bond lengths and angle in the dication are normal (Rother et al., 1997 ▸; Gatfaoui et al., 2014 ▸; Essid et al., 2015 ▸).

Figure 1.

An ORTEP view of (I) with displacement ellipsoids drawn at the 30% probability level. Symmetry code: (i) −x + , −y + , −z.

The perchlorate anion displays its expected tetra­hedral geometry around the chlorine atom. Inter­atomic bond lengths and angles of the perchlorate anion lie respectively within the ranges [1.4327 (10)–1.4452 (11) Å] and [109.01 (7)- 110.28 (7) °]. Similar geometrical features have also been noticed in other crystal structures (Toumi Akriche et al., 2010 ▸; Berrah et al., 2012 ▸).

Supra­molecular features  

In the extended structure, the anions are connected to the water mol­ecules through O_w—H⋯O hydrogen bonds (Table 1 ▸), generating a corrugated (5) chain running along the [010] direction (Fig. 2 ▸). These chains are linked via the trans-2,5-dimethlpiperazine-1,4-diium cations through N—H⋯O, N—H⋯O_w and weak C—H⋯O hydrogen bonds, forming a three-dimensional supra­molecular network (Fig. 3 ▸). These data show that each organic cation is connected to six inorganic chains.

Table 1. Hydrogen-bond geometry (Å, °).

D—H⋯A	D—H	H⋯A	D⋯A	D—H⋯A
OW—H1W⋯O1i	0.85 (1)	2.03 (1)	2.8637 (16)	167 (2)
OW—H2W⋯O2ii	0.85 (1)	2.23 (1)	2.9932 (16)	150 (2)
N1—H1N⋯O4iii	0.90	2.18	2.9067 (15)	137
N1—H1N⋯O3iv	0.90	2.42	3.0293 (15)	125
N1—H1N⋯OW v	0.90	2.55	3.1994 (16)	130
N1—H2N⋯OW i	0.90	1.91	2.8019 (15)	172
C1—H1B⋯O3iv	0.97	2.56	3.1007 (17)	116

Symmetry codes: (i) ; (ii) ; (iii) ; (iv) ; (v) .

Figure 2.

Hydrogen-bonded supra­molecular chains involving anions and water mol­ecules of compound (I), represented through the ab plane.

Figure 3.

Projection of (I) along the b axis. The H-atoms not involved in hydrogen bonding are omitted.

Hirshfeld surface analysis  

The three-dimensional Hirshfeld surfaces and two-dimensional fingerprint plots of (I) were prepared using CrystalExplorer (Wolff et al., 2012 ▸) and are shown in Figs. 4 ▸ and 5 ▸, respectively. The inter­action between N—H and oxygen atoms can be seen in the Hirshfeld surface as the bright-red area in Fig. 4 ▸ (labeled a). The light-red spots are due to O_w—H⋯O inter­actions (labeled b). For the salt, O⋯H/H⋯O contacts, which are attributed to N—H⋯O_w and O_w—H⋯O hydrogen-bonding inter­actions, appear as two sharp symmetric spikes in the two-dimensional fingerprint maps. They have the most significant contribution to the total Hirshfeld surfaces. The H⋯H contacts appear in the middle of the scattered points in the two-dimensional fingerprint maps. For further information on Hirshfeld surfaces, see: Spackman & McKinnon (2002 ▸) and Spackman & Jayatilaka (2009 ▸).

Figure 4.

Hirshfeld surface around the constituents of (I) coloured according to d _norm. The surfaces are shown as transparent to allow visualization of the orientation and conformation of the functional groups.

Figure 5.

Fingerprint plots of the major contacts: (a) H⋯O and (b) H⋯H.

Synthesis and crystallization  

The title compound was prepared from an alcoholic solution containing trans-2,5-di­methyl­piparazine (0.1 g, 1 mmol, purity 99%, Aldrich) dissolved in ethanol (20 ml) and perchloric acid HClO₄ (0.2 g, 2 mmol, purity 96%, Aldrich) with a molar ratio of 1:2. This mixture was stirred for 1 h. After a week of evaporation at room temperature, colorless single crystals of suitable dimensions for crystallographic study were formed, and were isolated by filtration and washed with a small amount of distilled water. The crystals can be stable for months under normal conditions of temperature and humidity.

Refinement  

Crystal data, data collection and structure refinement details are summarized in Table 2 ▸. All H atoms were located in a difference map but were placed geometrically and refined using a riding model, with C—H = 0.96 Å (meth­yl), or 0.98 Å (methine), N—H = 0.90 Å (NH₂) with U _iso(H) = 1.2U _eq(C or N). The H atoms of the water mol­ecule were refined with a distance restraint of O—H = 0.85 (1) Å using DFIX and DANG commands (Sheldrick, 2015 ▸) with U _iso(H) = 1.5U _eq(O).

Table 2. Experimental details.

Crystal data
Chemical formula	C6H16N2 2+·2ClO4 −·2H2O
M r	351.14
Crystal system, space group	Monoclinic, C2/c
Temperature (K)	150
a, b, c (Å)	16.8603 (8), 7.2655 (3), 14.4534 (6)
β (°)	128.751 (1)
V (Å3)	1380.78 (10)
Z	4
Radiation type	Mo Kα
μ (mm−1)	0.52
Crystal size (mm)	0.44 × 0.29 × 0.25
Data collection
Diffractometer	Bruker D8 VENTURE
Absorption correction	Multi-scan (SADABS; Bruker, 2014 ▸)
T min, T max	0.775, 0.878
No. of measured, independent and observed [I > 2σ(I)] reflections	7760, 1557, 1457
R int	0.023
(sin θ/λ)max (Å−1)	0.649
Refinement
R[F 2 > 2σ(F 2)], wR(F 2), S	0.028, 0.074, 1.13
No. of reflections	1557
No. of parameters	100
No. of restraints	3
H-atom treatment	H atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å−3)	0.34, −0.41

Computer programs: APEX2 and SAINT (Bruker, 2014 ▸), SIR97 (Altomare et al., 1999 ▸), SHELXL2014/7 (Sheldrick, 2015 ▸), ORTEP-3 for Windows and WinGX publication routines (Farrugia, 2012 ▸).

Supplementary Material

CCDC reference: 1470800

Additional supporting information: crystallographic information; 3D view; checkCIF report

supplementary crystallographic information

Crystal data

C6H16N22+·2ClO4−·2H2O	F(000) = 736
Mr = 351.14	Dx = 1.689 Mg m−3
Monoclinic, C2/c	Mo Kα radiation, λ = 0.71073 Å
a = 16.8603 (8) Å	Cell parameters from 7552 reflections
b = 7.2655 (3) Å	θ = 3.1–27.5°
c = 14.4534 (6) Å	µ = 0.52 mm−1
β = 128.751 (1)°	T = 150 K
V = 1380.78 (10) Å3	Prism, colourless
Z = 4	0.44 × 0.29 × 0.25 mm

Data collection

D8 VENTURE Bruker AXS diffractometer	1557 independent reflections
Radiation source: Incoatec microfocus sealed tube	1457 reflections with I > 2σ(I)
Multilayer monochromator	Rint = 0.023
rotation images scans	θmax = 27.5°, θmin = 3.1°
Absorption correction: multi-scan (SADABS; Bruker, 2014)	h = −21→21
Tmin = 0.775, Tmax = 0.878	k = −9→9
7760 measured reflections	l = −18→15

Refinement

Refinement on F2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.028	Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.074	H atoms treated by a mixture of independent and constrained refinement
S = 1.13	w = 1/[σ2(Fo2) + (0.0308P)2 + 1.9533P] where P = (Fo2 + 2Fc2)/3
1557 reflections	(Δ/σ)max = 0.001
100 parameters	Δρmax = 0.34 e Å−3
3 restraints	Δρmin = −0.41 e Å−3

Special details

Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Ų)

	x	y	z	Uiso*/Ueq
Cl1	0.09748 (2)	0.13197 (4)	0.16201 (3)	0.01195 (12)
O1	0.14991 (10)	0.26958 (16)	0.25415 (10)	0.0307 (3)
O2	0.16959 (8)	−0.00473 (16)	0.18348 (11)	0.0254 (3)
O3	0.02214 (9)	0.04530 (16)	0.16384 (10)	0.0239 (3)
O4	0.05035 (9)	0.21898 (16)	0.04934 (9)	0.0236 (3)
OW	0.40676 (9)	0.84994 (14)	0.78311 (9)	0.0203 (2)
H1W	0.3881 (18)	0.9600 (15)	0.780 (2)	0.046 (7)*
H2W	0.3837 (15)	0.780 (2)	0.8086 (18)	0.034 (6)*
N1	0.14181 (8)	0.75580 (15)	0.43347 (10)	0.0111 (2)
H2N	0.1201	0.7208	0.3612	0.013*
H1N	0.0867	0.7774	0.4286	0.013*
C1	0.20218 (10)	0.92935 (18)	0.46870 (12)	0.0119 (3)
H1A	0.2220	0.9720	0.5442	0.014*
H1B	0.1605	1.0239	0.4099	0.014*
C2	0.20319 (10)	0.60230 (18)	0.52072 (11)	0.0114 (3)
H2	0.2243	0.6396	0.5984	0.014*
C3	0.13915 (11)	0.42938 (19)	0.48147 (13)	0.0186 (3)
H3A	0.0801	0.4542	0.4754	0.028*
H3B	0.1785	0.3334	0.5385	0.028*
H3C	0.1183	0.3911	0.4056	0.028*

Atomic displacement parameters (Ų)

	U11	U22	U33	U12	U13	U23
Cl1	0.01181 (18)	0.01242 (18)	0.01379 (18)	−0.00022 (10)	0.00907 (14)	0.00166 (10)
O1	0.0321 (6)	0.0200 (6)	0.0225 (6)	−0.0075 (5)	0.0085 (5)	−0.0069 (5)
O2	0.0215 (6)	0.0256 (6)	0.0347 (6)	0.0119 (5)	0.0203 (5)	0.0101 (5)
O3	0.0246 (6)	0.0246 (6)	0.0358 (6)	−0.0064 (4)	0.0253 (5)	−0.0012 (5)
O4	0.0269 (6)	0.0308 (6)	0.0190 (5)	0.0105 (5)	0.0171 (5)	0.0119 (4)
OW	0.0272 (6)	0.0152 (5)	0.0174 (5)	−0.0013 (4)	0.0135 (5)	0.0000 (4)
N1	0.0077 (5)	0.0131 (5)	0.0124 (5)	0.0006 (4)	0.0062 (4)	0.0008 (4)
C1	0.0120 (6)	0.0101 (6)	0.0142 (6)	0.0011 (5)	0.0084 (5)	0.0006 (5)
C2	0.0110 (6)	0.0113 (6)	0.0122 (6)	0.0008 (5)	0.0074 (5)	0.0020 (5)
C3	0.0163 (6)	0.0139 (6)	0.0230 (7)	−0.0034 (5)	0.0111 (6)	0.0008 (5)

Geometric parameters (Å, º)

Cl1—O3	1.4327 (10)	C1—C2i	1.5218 (17)
Cl1—O4	1.4363 (10)	C1—H1A	0.9700
Cl1—O1	1.4425 (11)	C1—H1B	0.9700
Cl1—O2	1.4452 (11)	C2—C3	1.5163 (18)
OW—H1W	0.850 (9)	C2—C1i	1.5218 (17)
OW—H2W	0.850 (9)	C2—H2	0.9800
N1—C1	1.4955 (16)	C3—H3A	0.9600
N1—C2	1.5071 (16)	C3—H3B	0.9600
N1—H2N	0.9000	C3—H3C	0.9600
N1—H1N	0.9000
O3—Cl1—O4	110.28 (7)	N1—C1—H1B	109.5
O3—Cl1—O1	109.01 (7)	C2i—C1—H1B	109.5
O4—Cl1—O1	109.03 (7)	H1A—C1—H1B	108.1
O3—Cl1—O2	109.29 (7)	N1—C2—C3	110.17 (10)
O4—Cl1—O2	109.87 (7)	N1—C2—C1i	108.88 (10)
O1—Cl1—O2	109.34 (7)	C3—C2—C1i	111.63 (11)
H1W—OW—H2W	109.1 (17)	N1—C2—H2	108.7
C1—N1—C2	111.99 (10)	C3—C2—H2	108.7
C1—N1—H2N	109.2	C1i—C2—H2	108.7
C2—N1—H2N	109.2	C2—C3—H3A	109.5
C1—N1—H1N	109.2	C2—C3—H3B	109.5
C2—N1—H1N	109.2	H3A—C3—H3B	109.5
H2N—N1—H1N	107.9	C2—C3—H3C	109.5
N1—C1—C2i	110.74 (10)	H3A—C3—H3C	109.5
N1—C1—H1A	109.5	H3B—C3—H3C	109.5
C2i—C1—H1A	109.5

Symmetry code: (i) −x+1/2, −y+3/2, −z+1.

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
OW—H1W···O1i	0.85 (1)	2.03 (1)	2.8637 (16)	167 (2)
OW—H2W···O2ii	0.85 (1)	2.23 (1)	2.9932 (16)	150 (2)
N1—H1N···O4iii	0.90	2.18	2.9067 (15)	137
N1—H1N···O3iv	0.90	2.42	3.0293 (15)	125
N1—H1N···OWv	0.90	2.55	3.1994 (16)	130
N1—H2N···OWi	0.90	1.91	2.8019 (15)	172
C1—H1B···O3iv	0.97	2.56	3.1007 (17)	116

Symmetry codes: (i) −x+1/2, −y+3/2, −z+1; (ii) −x+1/2, −y+1/2, −z+1; (iii) x, −y+1, z+1/2; (iv) −x, y+1, −z+1/2; (v) x−1/2, −y+3/2, z−1/2.